From a5b9e03485fa539846a8288137332ae124760064 Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Thu, 5 Nov 2020 15:01:10 +1100
Subject: add slide on bionix

---
 slides.tex | 24 +++++++++++++++++++-----
 1 file changed, 19 insertions(+), 5 deletions(-)

diff --git a/slides.tex b/slides.tex
index ec14f08..fc09a6d 100644
--- a/slides.tex
+++ b/slides.tex
@@ -113,13 +113,15 @@
   \end{minipage}
 \end{frame}
 
+\againframe<4>{dag}
+
 \begin{frame}
   \frametitle{BioNix contributions}
   \begin{enumerate}
     \item Builds on Nix, a robust functional package manager
-    \item Manages both software and workflows within the one system
+    \item Manages both software, data, and workflows within the one system
     \item Implicitly specifies its entire computational environment
-    \item Simple, purely functional domain-specific language, simplifying specifying workflows
+    \item Purely functional domain-specific language, simplifying specifying workflows
       to function composition
     \item Typing to reduce errors~\autocite{Bed2019}
   \end{enumerate}
@@ -130,10 +132,24 @@
   \begin{enumerate}
     \item Simple configuration language (like JSON + functions)
     \item Build engine that \emph{realises} \emph{derivations}
+      \begin{itemize}
+        \item resumption
+        \item error handling
+        \item logging
+        \item parallelisation
+      \end{itemize}
     \item Derivations are complete descriptions for producing build products: all inputs and a build recipe
     \item Controlled \emph{side effects}\footnote{stuff not captured by the derivation}: none allowed during a build
     \item Output location unique and determined by hashing the derivation: i.e., hash based version management
-    \item Deterministic $\Rightarrow$ reproducible
+  \end{enumerate}
+\end{frame}
+
+\begin{frame}
+  \frametitle{What is BioNix?}
+  \begin{enumerate}
+    \item Thin wrapper on Nix
+    \item Models \emph{stages}\footnote{the execution of one or more executables on one or more input files, producing one or more output files.} as functions (\texttt{config → inputs → drv})
+    \item Library of bioinformatics tools (BWA, samtools, etc)
   \end{enumerate}
 \end{frame}
 
@@ -151,8 +167,6 @@
   \end{minipage}
 \end{frame}
 
-\againframe<4>{dag}
-
 \begin{frame}
   \frametitle{Demo}
   \pause
-- 
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